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rDNA sequences

Barbara Dunn bdunn at GENOME.STANFORD.EDU
Mon Aug 21 19:27:00 EST 1995


On 14 Aug 1995, Quintin Rascon Cruz wrote:

> Dear Neters..
>     We are working on rDNA of yeasts, but  I cant find identification 
> number  to get complete secuence of rDNA aprox  10kb of the newest 
> modification of the secuence. cud you sent e-mail  to me pleas.
> regards
> 
> Quintin Rascon Cruz
> Facultad de Ciencias Quimicas
> Depto. Inmunologia
> Apo. postal 1542-C
> Chihuahua Chihuahua. Mexico.
> Tel. (14) 13-18-28  Fax. (14) 14-44-49
> Casa. (14) 25-05-24
> Email  a55595 at uachih.uachnet.mx

I work with the Saccharomyces Genome Database, and thought I might be able
to help you a bit with your question. 

The sequence of the rDNA locus is not yet available as one complete unit
from GenBank, so you have to piece it together from a set of overlapping
sequences.  In our database, we have assembled the overlapping sequences
for the 18S, 5.8S, 25S, 5S and 37S rDNA sequences into one contiguous
sequence that is 8503 bp in length.  The name of this assembled sequence
is "cseqXII_07".  If you would like to view this sequence (and export it
into your files) you can access the Saccharomyces database through either
the WWW (WorldWideWeb) or Gopher, using the addresses given below.  If you
access our Gopher "home page", you would select option 5 (Saccharomyces
Information), then select option 2 (Saccharomyces Genome Database), then
enter in "cseqXII_07" as the search term; at this point you get a (long)
list of all the items in the database in which "cseqXII_07" is
mentioned...you want to select option 158 (DNA : "cseq XII_07 (SGD)"), at
which point all 8503 bp of DNA sequence is displayed.  You can then enter
in a "?" to get a menu of things you can do with the DNA sequence (such as
"s" to save it into a file or "p" to print it).  The process is similar if
you access us through the Web home page. 

The Saccharomyces systematic sequencing effort will probably have
completed sequencing the entire genome by the end of this year (with all
of it publicly available by the spring of '96), at which point the
sequence of the entire rDNA region will be available.  Mark Johnston's lab
is sequencing the rDNA region, and he may be willing to give you their
sequence for it, even though it is not yet publicly available.  You can
e-mail him at "mj at sequencer.wustl.edu". 

    Barbara Dunn, Ph.D.
    Database Curator                    
    Saccharomyces Genome Database                                
    Department of Genetics                                     
    Stanford University Med. Ctr.                         
    Stanford, CA  94305-5120   USA 
    phone: 415-725-8956                                   
    fax:   415-723-7016                                   
                                                       
    e-mail:        bdunn at genome.stanford.edu	
								
    Internet contacts for Sacch. Genome Database--		
    e-mail:	yeast-curator at genome.stanford.edu	
    Gopher:	genome-gopher.stanford.edu		
    WWW:	http://genome-www.stanford.edu/		
    ftp:	genome-ftp.stanford.edu			






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